To clarify:
Indesign 2.x does not support direct to PDF/X-3. ID CS does.
Scribus has had this since 0.9.5 - 02 Jan. 2003 See: http://web2.altmuehlnet.de/fschmid/ChangeLog
At that time, neither Acrobat 6, nor ID CS were released. So yes, Scribus was the first DTP/layout app to support PDF/X-3